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Add path regexing #668

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Feb 8, 2024
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63 changes: 63 additions & 0 deletions docker/user.Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
# Install ubuntu 20.04
FROM ubuntu:20.04
LABEL maintainer="[email protected]"
LABEL version="0.0"
LABEL description="Hermes Docker image with CI"

# Disable Prompt During Packages Installation
ARG DEBIAN_FRONTEND=noninteractive

# Update ubuntu
SHELL ["/bin/bash", "-c"]
RUN apt update && apt install

# Install some basic packages
RUN apt install -y \
openssh-server \
sudo \
git \
gcc g++ gfortran make binutils gpg \
tar zip xz-utils bzip2 \
perl m4 libncurses5-dev libxml2-dev diffutils \
pkg-config cmake pkg-config \
python3 python3-pip doxygen \
lcov zlib1g-dev hdf5-tools \
build-essential ca-certificates \
coreutils curl environment-modules \
gfortran git gpg lsb-release python3 python3-distutils \
python3-venv unzip zip \
bash jq python gdbserver gdb

# Setup basic environment
ENV USER="root"
ENV HOME="/root"
ENV SPACK_DIR="${HOME}/spack"
ENV SPACK_VERSION="v0.20.2"
ENV HERMES_DEPS_DIR="${HOME}/hermes_deps"
ENV HERMES_DIR="${HOME}/hermes"
COPY ci/module_load.sh /module_load.sh

# Install Spack
RUN . /module_load.sh && \
git clone -b ${SPACK_VERSION} https://github.com/spack/spack ${SPACK_DIR} && \
. "${SPACK_DIR}/share/spack/setup-env.sh" && \
git clone -b dev https://github.com/lukemartinlogan/hermes.git ${HERMES_DEPS_DIR} && \
# git clone -b dev https://github.com/HDFGroup/hermes.git ${HERMES_DEPS_DIR} && \
spack repo add ${HERMES_DEPS_DIR}/ci/hermes && \
mkdir -p ${HERMES_DIR} && \
spack external find

# Install hermes
RUN . /module_load.sh && \
. "${SPACK_DIR}/share/spack/setup-env.sh" && \
spack install hermes@master+vfd+mpiio^[email protected]

# Install jarvis-cd
RUN git clone https://github.com/grc-iit/jarvis-cd.git && \
cd jarvis-cd && \
pip install -e . -r requirements.txt

# Install scspkg
RUN git clone https://github.com/grc-iit/scspkg.git && \
cd scspkg && \
pip install -e . -r requirements.txt
2 changes: 1 addition & 1 deletion hermes_adapters/filesystem/filesystem.h
Original file line number Diff line number Diff line change
Expand Up @@ -692,7 +692,7 @@ class Filesystem : public FilesystemIoClient {
auto &paths = HERMES_CLIENT_CONF.path_list_;
// Check if path is included or excluded
for (config::UserPathInfo &pth : paths) {
if (abs_path.rfind(pth.path_) != std::string::npos) {
if (pth.Match(abs_path)) {
if (abs_path == pth.path_ && pth.is_directory_) {
// Do not include if path is a tracked directory
return false;
Expand Down
3 changes: 1 addition & 2 deletions hermes_adapters/vfd/H5FDhermes.cc
Original file line number Diff line number Diff line change
Expand Up @@ -229,6 +229,7 @@ H5FD__hermes_term(void) {
static H5FD_t *
H5FD__hermes_open(const char *name, unsigned flags, hid_t fapl_id,
haddr_t maxaddr) {
TRANSPARENT_HERMES();
H5FD_hermes_t *file = NULL; /* hermes VFD info */
int fd = -1;
int o_flags = 0;
Expand Down Expand Up @@ -516,13 +517,11 @@ static herr_t H5FD__hermes_write(H5FD_t *_file, H5FD_mem_t type,
*/
H5PL_type_t
H5PLget_plugin_type(void) {
TRANSPARENT_HERMES();
return H5PL_TYPE_VFD;
}

const void*
H5PLget_plugin_info(void) {
TRANSPARENT_HERMES();
return &H5FD_hermes_g;
}

Expand Down
85 changes: 0 additions & 85 deletions include/hermes/adapter_types.h

This file was deleted.

31 changes: 30 additions & 1 deletion include/hermes/config_client.h
Original file line number Diff line number Diff line change
Expand Up @@ -34,16 +34,45 @@ static inline const bool do_exclude = false;

/** Stores information about path inclusions and exclusions */
struct UserPathInfo {
std::regex regex_; /**< The regex to match the path */
std::string path_; /**< The path the user specified */
bool include_; /**< Whether to track path. */
bool is_directory_; /**< Whether the path is a file or directory */

/** Default constructor */
UserPathInfo() = default;

static std::string ToRegex(const std::string &path) {
std::string regex_pattern = "^";
for (char c : path) {
if (c == '.') {
regex_pattern += "\\.";
} else if (c == '/') {
regex_pattern += "\\/";
} else if (c == '*') {
regex_pattern += ".*";
} else {
regex_pattern += c;
}
}
return regex_pattern;
}

/** Emplace Constructor */
UserPathInfo(const std::string &path, bool include, bool is_directory)
: path_(path), include_(include), is_directory_(is_directory) {}
: path_(path), include_(include), is_directory_(is_directory) {
std::string regex_pattern = ToRegex(path);
if (is_directory) {
regex_pattern += ".*";
}
regex_ = std::regex(regex_pattern);
}

/** Detect if a path matches the input path */
bool Match(const std::string &abs_path) {
return std::regex_match(abs_path, regex_);
// return abs_path.rfind(path_) != std::string::npos;
}
};

/**
Expand Down
1 change: 1 addition & 0 deletions test/unit/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ set(CMAKE_CXX_STANDARD 17)
include_directories(${CMAKE_CURRENT_SOURCE_DIR})
include_directories(${CMAKE_SOURCE_DIR}/tasks/hrun_admin/include)
add_subdirectory(ipc)
add_subdirectory(config)
add_subdirectory(hermes)
add_subdirectory(hermes_adapters)
add_subdirectory(boost)
45 changes: 45 additions & 0 deletions test/unit/config/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
cmake_minimum_required(VERSION 3.10)
project(hermes)

set(CMAKE_CXX_STANDARD 17)

#------------------------------------------------------------------------------
# Build Tests
#------------------------------------------------------------------------------

add_executable(test_config_exec
${TEST_MAIN}/main_mpi.cc
test_init.cc
test_config.cc
)
add_dependencies(test_config_exec
${Hermes_CLIENT_DEPS} hermes)
target_link_libraries(test_config_exec
${Hermes_CLIENT_LIBRARIES} hermes Catch2::Catch2 MPI::MPI_CXX)
jarvis_test(hermes test_hermes)

#------------------------------------------------------------------------------
# Test Cases
#------------------------------------------------------------------------------

# STRING TESTS
#add_test(NAME test_ipc COMMAND
# ${CMAKE_BINARY_DIR}/bin/test_messages "TestIpc")

#------------------------------------------------------------------------------
# Install Targets
#------------------------------------------------------------------------------
install(TARGETS
test_config_exec
EXPORT
${HERMES_EXPORTED_TARGETS}
LIBRARY DESTINATION ${HERMES_INSTALL_LIB_DIR}
ARCHIVE DESTINATION ${HERMES_INSTALL_LIB_DIR}
RUNTIME DESTINATION ${HERMES_INSTALL_BIN_DIR})

#-----------------------------------------------------------------------------
# Coverage
#-----------------------------------------------------------------------------
if(HERMES_ENABLE_COVERAGE)
set_coverage_flags(test_config_exec)
endif()
42 changes: 42 additions & 0 deletions test/unit/config/test_config.cc
Original file line number Diff line number Diff line change
@@ -0,0 +1,42 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Distributed under BSD 3-Clause license. *
* Copyright by The HDF Group. *
* Copyright by the Illinois Institute of Technology. *
* All rights reserved. *
* *
* This file is part of Hermes. The full Hermes copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the top directory. If you do not *
* have access to the file, you may request a copy from [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#include "basic_test.h"
#include "hrun/api/hrun_client.h"
#include "hrun_admin/hrun_admin.h"
#include "hermes/hermes.h"
#include "hermes/bucket.h"
#include "data_stager/factory/binary_stager.h"
#include <mpi.h>

TEST_CASE("TestHermesPaths") {
PAGE_DIVIDE("Directory path") {
hermes::config::UserPathInfo info("/home/hello", true, true);
REQUIRE(info.Match("/home") == false);
REQUIRE(info.Match("/home/hello") == true);
REQUIRE(info.Match("/home/hello/hi.txt") == true);
}

PAGE_DIVIDE("Simple path") {
hermes::config::UserPathInfo info("/home/hello.txt", true, false);
REQUIRE(info.Match("/home/hello") == false);
REQUIRE(info.Match("/home/hello.txt") == true);
}

PAGE_DIVIDE("Wildcard path") {
hermes::config::UserPathInfo info("/home/hello/*.json", true, false);
REQUIRE(info.Match("/home/hello") == false);
REQUIRE(info.Match("/home/hello/hi.json") == true);
REQUIRE(info.Match("/home/hello/.json") == true);
}
}

22 changes: 22 additions & 0 deletions test/unit/config/test_init.cc
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Distributed under BSD 3-Clause license. *
* Copyright by The HDF Group. *
* Copyright by the Illinois Institute of Technology. *
* All rights reserved. *
* *
* This file is part of Hermes. The full Hermes copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the top directory. If you do not *
* have access to the file, you may request a copy from [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */


#include "hrun/api/hrun_client.h"
#include "basic_test.h"
#include "test_init.h"

void MainPretest() {
}

void MainPosttest() {
}
19 changes: 19 additions & 0 deletions test/unit/config/test_init.h
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Distributed under BSD 3-Clause license. *
* Copyright by The HDF Group. *
* Copyright by the Illinois Institute of Technology. *
* All rights reserved. *
* *
* This file is part of Hermes. The full Hermes copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the top directory. If you do not *
* have access to the file, you may request a copy from [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */


#ifndef HRUN_TEST_UNIT_IPC_TEST_INIT_H_
#define HRUN_TEST_UNIT_IPC_TEST_INIT_H_

#include "hrun/hrun_types.h"

#endif // HRUN_TEST_UNIT_IPC_TEST_INIT_H_
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